Coloring only specific pixels

Question

I have a matrix representing an image of brain with each (i,j) position having a value between 0 and 1. I am applying a color map, so that those pixels with value 1 are red and

Answer 1

You can do this by plotting a surf(-ace) and passing in alpha values as follows.

brain = ... % background brain image
data = ...  % the data you are trying to overlay
imshow(brain);
hold on;
surf(zeros(size(data)), data, 'AlphaData', data > 0.8);
colormap(...); % whatever colormap you like

Have a look at the surface properties documentation for more options you can pass to surf.

Answer 2

Here is another option, create a 3-layers array replicating your grayscale brain image (imagesc will scale each layer similarly resulting in equal r, g, and b values -> levels of gray).

GrayBckgnd = repmat(brain, [1, 1, 3]);
data = …

Then overlay it with the activity data:

imagesc(GrayBcknd);
hold on;
DataImg = imagesc(data);
set(DataImg, 'AlphaData', im2double(data>0.8));
colormap jet; % or any other colormap.